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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/28424528/elucidation-of-quantitative-structural-diversity-of-remarkable-rearrangement-regions-shufflons-in-inci2-plasmids
#1
Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424085/the-within-host-population-dynamics-of-mycobacterium-tuberculosis-vary-with-treatment-efficacy
#2
Andrej Trauner, Qingyun Liu, Laura E Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sebastien Gagneux, Clifton E Barry, Qian Gao
BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics...
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28417189/draft-genome-sequence-of-a-biosurfactant-producing-bacillus-subtilis-umx-103-isolated-from-hydrocarbon-contaminated-soil-in-terengganu-malaysia
#3
Yousri Abdelmutalab Abdelhafiz, Thamilvaani Manaharan, Saharuddin BinMohamad, Amir Feisal Merican
The draft genome here presents the sequence of Bacillus subtilis UMX-103. The bacterial strain was isolated from hydrocarbon-contaminated soil from Terengganu, Malaysia. The whole genome of the bacterium was sequenced using Illumina HiSeq 2000 sequencing platform. The genome was assembled using de novo approach. The genome size of UMX-103 is 4,234,627 bp with 4399 genes comprising 4301 protein-coding genes and 98 RNA genes. The analysis of assembled genes revealed the presence of 25 genes involved in biosurfactant production, where 14 of the genes are related to biosynthesis and 11 of the genes are in the regulation of biosurfactant productions...
April 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28414633/genome-wide-analysis-provides-evidence-on-the-genetic-relatedness-of-the-emergent-xylella-fastidiosa-genotype-in-italy-to-isolates-from-central-america
#4
Annalisa Giampetruzzi, Maria Saponari, Giuliana Loconsole, Donato Boscia, Vito Nicola Savino, Rodrigo Almeida, Stefania Zicca, Blanca Landa, Carlos Chacon Diaz, Pasquale Saldarelli
Xylella fastidiosa is a plant pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles which are monophyletic with those of subsp. pauca in South America...
April 17, 2017: Phytopathology
https://www.readbyqxmd.com/read/28411226/the-current-state-of-macrolide-resistance-in-campylobacter-a-review-of-trends-and-impacts-of-resistance-mechanisms
#5
Hannah Bolinger, Sophia Kathariou
Campylobacter spp., especially Campylobacter jejuni and C. coli, are leading bacterial foodborne pathogens worldwide. In the United States, an estimated 0.8 million cases of campylobacteriosis occur annually, mostly involving C. jejuni. Campylobacteriosis is generally self-limiting but in severe cases treatment with antibiotics may be mandated. Increasing incidence of fluoroquinolone resistance in Campylobacter has rendered macrolides like erythromycin and azithromycin the drugs of choice for human campylobacteriosis...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28410416/correction-a-year-of-infection-in-the-intensive-care-unit-prospective-whole-genome-sequencing-of-bacterial-clinical-isolates-reveals-cryptic-transmissions-and-novel-microbiota
#6
David J Roach, Joshua N Burton, Choli Lee, Bethany Stackhouse, Susan M Butler-Wu, Brad T Cookson, Jay Shendure, Stephen J Salipante
[This corrects the article DOI: 10.1371/journal.pgen.1005413.].
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28407967/molecular-characterization-of-an-unauthorized-genetically-modified-bacillus-subtilis-production-strain-identified-in-a-vitamin-b2-feed-additive
#7
Valentina Paracchini, Mauro Petrillo, Ralf Reiting, Alexandre Angers-Loustau, Daniela Wahler, Andrea Stolz, Birgit Schönig, Anastasia Matthies, Joachim Bendiek, Dominik M Meinel, Sven Pecoraro, Ulrich Busch, Alex Patak, Joachim Kreysa, Lutz Grohmann
Many food and feed additives result from fermentation of genetically modified (GM) microorganisms. For vitamin B2 (riboflavin), GM Bacillus subtilis production strains have been developed and are often used. The presence of neither the GM strain nor its recombinant DNA is allowed for fermentation products placed on the EU market as food or feed additive. A vitamin B2 product (80% feed grade) imported from China was analysed. Viable B. subtilis cells were identified and DNAs of two bacterial isolates (LHL and LGL) were subjected to three whole genome sequencing (WGS) runs with different devices (MiSeq, 454 or HiSeq system)...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28397974/genome-resequencing-analysis-of-salmonella-typhimurium-lt-2-strains-ta98-and-ta100-for-the-establishment-of-a-next-generation-sequencing-based-mutagenicity-assay
#8
Shoji Matsumura, Yuichi Ito, Osamu Morita, Hiroshi Honda
Next-generation sequencing (NGS) is a potentially useful technology to achieve a more precise evaluation of chemical mutagenicity. To establish NGS-based mutagenicity assays, which enable the direct detection of chemically induced mutations in a whole genome manner, the selection of appropriate biological resources and their precise genome sequences are essential. Here, we performed genome re-sequencing analyses of Salmonella typhimurium LT-2 strains TA98 and TA100, which have been frequently used in mutagenicity assays...
April 11, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28393289/practically-delineating-bacterial-species-with-genealogical-concordance
#9
Stephanus N Venter, Marike Palmer, Chrizelle W Beukes, Wai-Yin Chan, Giyoon Shin, Elritha van Zyl, Tarren Seale, Teresa A Coutinho, Emma T Steenkamp
Bacterial species are commonly defined by applying a set of predetermined criteria, including DNA-DNA hybridization values, 16S rRNA gene sequence similarity, phenotypic data as well as genome-based criteria such as average nucleotide identity or digital DNA-DNA hybridization. These criteria mostly allow for the delimitation of taxa that resemble typical bacterial species. Their application is often complicated when the objective is to delineate new species that are characterized by significant population-level diversity or recent speciation...
April 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28391484/genomic-and-molecular-characterization-of-a-novel-quorum-sensing-molecule-in-bacillus-licheniformis
#10
Elham Esmaeilishirazifard, Daniela De Vizio, Sterghios A Moschos, Tajalli Keshavarz
Quorum sensing molecules (QSMs) are involved in the regulation of complicated processes helping bacterial populations respond to changes in their cell-density. Although the QS gene cluster (comQXPA) has been identified in the genome sequence of some bacilli, the QS system B. licheniformis has not been investigated in detail, and its QSM (ComX pheromone) has not been identified. Given the importance of this antagonistic bacterium as an industrial workhorse, this study was aimed to elucidate B. licheniformis NCIMB-8874 QS...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28388689/whole-genome-sequencing-of-brucella-melitensis-isolated-from-57-patients-in-germany-reveals-high-diversity-in-strains-from-middle-east
#11
Enrico Georgi, Mathias C Walter, Marie-Theres Pfalzgraf, Bernd H Northoff, Lesca M Holdt, Holger C Scholz, Lothar Zoeller, Sabine Zange, Markus H Antwerpen
Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare in Northern and Western Europe. However, since 2014 a significant increase of imported infections caused by Brucella (B.) melitensis has been noticed in Germany. Patients predominantly originated from Middle East including Turkey and Syria. These circumstances afforded an opportunity to gain insights into the population structure of Brucella strains. Brucella-isolates from 57 patients were recovered between January 2014 and June 2016 with culture confirmed brucellosis by the National Consultant Laboratory for Brucella...
2017: PloS One
https://www.readbyqxmd.com/read/28381609/the-modified-carbapenem-inactivation-method-mcim-for-phenotypic-detection-of-carbapenemase-production-among-enterobacteriaceae
#12
Virginia M Pierce, Patricia J Simner, David R Lonsway, Darcie E Roe-Carpenter, J Kristie Johnson, William B Brasso, April M Bobenchik, Zabrina C Lockett, Angella Charnot-Katsikas, Mary Jane Ferraro, Richard B Thomson, Stephen G Jenkins, Brandi M Limbago, Sanchita Das
The ability of clinical microbiology laboratories to reliably detect carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is an important element of the effort to prevent and contain the spread of these pathogens and an integral part of antimicrobial stewardship. Existing methods each have limitations. A new, straightforward, inexpensive, and specific phenotypic method for the detection of carbapenemase production, the carbapenem inactivation method (CIM), was recently described. Here we describe a two-stage evaluation of a modified carbapenem inactivation method (mCIM), in which tryptic soy broth was substituted for water during the inactivation step and the length of this incubation was extended...
April 5, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28381604/a-target-specific-assay-for-rapid-and-quantitative-detection-of-mycobacterium-chimaera-dna
#13
Enrique Zozaya-Valdés, Jessica L Porter, John Coventry, Janet A M Fyfe, Glen P Carter, Anders Gonçalves da Silva, Mark B Schultz, Torsten Seemann, Paul D R Johnson, Andrew J Stewardson, Ivan Bastian, Sally A Roberts, Benjamin P Howden, Deborah A Williamson, Timothy P Stinear
Mycobacterium chimaera is an opportunistic environmental mycobacterium, belonging to the Mycobacterium intracellulare complex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasive M. chimaera infections following cardiac surgery. Investigations suggest world-wide spread of a specific M. chimaera clone, associated with contaminated hospital heater-cooler units used during the surgery. Given the global dissemination of this clone, its potential to cause invasive disease, and the laboriousness of current culture-based diagnostic methods, there is a pressing need to develop rapid and accurate diagnostic assays, specific for M...
April 5, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28381083/the-gut-microbiota-its-anatomy-and-physiology-during-all-life
#14
Giulia Gibiino, Gianluca Ianiro, Giovanni Cammarota, Antonio Gasbarrini
The wide assemblage of microorganisms inhabiting our gastrointestinal tract is an attractive field for overwhelming contemporary research in several aspects of the human health. Most recent molecular techniques, as the use of rRNAs or whole genome sequencing, definitely overcame traditional culture techniques in giving outline of the intestinal bacterial richness. Moreover, the crosstalk between host and intestinal microbes is considered a cornerstone affecting the host's metabolism, immunity, autoimmunity and autoinflammation and elaborate networks linked to several organs...
April 4, 2017: Minerva Gastroenterologica e Dietologica
https://www.readbyqxmd.com/read/28380509/identification-of-loci-associated-with-susceptibility-to-subspecies-tissue-infection-in-cattle
#15
J N Kiser, S N White, K A Johnson, J L Hoff, J F Taylor, H L Neibergs
Johne's disease is a contagious bacterial infection of cattle caused by ssp. (). A previous genome-wide association analysis (GWAA) in Holstein cattle identified QTL on BTA3 and BTA9 that were highly associated (P < 5 × 10) and on BTA1, BTA16, and BTA21 that were moderately associated (P < 5 × 10) with Map tissue infection. The objectives of this study were to validate previous GWAA results in Jersey cattle ( = 57), Holstein cattle from the Pacific Northwest (PNW, = 205) and a combined Holstein population from the PNW and the Northeast (PNW + NE, = 423), and also identify new loci associated with tissue infection...
March 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28373958/genome-centric-evaluation-of-burkholderia-sp-strain-srs-w-2-2016-resistant-to-high-concentrations-of-uranium-and-nickel-isolated-from-the-savannah-river-site-srs-usa
#16
Ashish Pathak, Ashvini Chauhan, Paul Stothard, Stefan Green, Mark Maienschein-Cline, Rajneesh Jaswal, John Seaman
Savannah River Site (SRS), an approximately 800-km(2) former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28373194/a-new-natural-product-analog-of-blasticidin-s-reveals-cellular-uptake-facilitated-by-the-nora-multidrug-transporter
#17
Jack R Davison, Katheryn M Lohith, Xiaoning Wang, Kostyantyn Bobyk, Sivakoteswara R Mandadapu, Su-Lin Lee, Regina Cencic, Justin Nelson, Scott Simpkins, Karen M Frank, Jerry Pelletier, Chad L Myers, Jeff Piotrowski, Harold E Smith, Carole A Bewley
The permeation of antibiotics through bacterial membranes to their target site is a crucial determinant of drug activity, but in many cases remains poorly understood. During screening efforts to discover new broad-spectrum antibiotic compounds from marine sponge samples, we identified a new analog of the peptidyl nucleoside antibiotic blasticidin S that exhibited up to 16-fold improved potency against a range of laboratory and clinical bacterial strains, which we named P10. Whole genome sequencing of laboratory-evolved strains of Staphylococcus aureus resistant to blasticidin S and P10, combined with genome-wide assessment of the fitness of barcoded Escherichia coli knockout strains in the presence of the antibiotics, revealed that the restriction of cellular access was a key feature in the development of resistance to this class of drug...
April 3, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28370938/mapping-of-homoeologous-chromosome-exchanges-influencing-quantitative-trait-variation-in-brassica-napus
#18
Anna Stein, Olivier Coriton, Mathieu Rousseau-Gueutin, Birgit Samans, Sarah V Schiessl, Christian Obermeier, Isobel A P Parkin, Anne-Marie Chèvre, Rod J Snowdon
Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to inter-homoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies...
March 29, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28368366/insights-on-klebsiella-pneumoniae-biofilms-assembled-on-different-surfaces-using-phenotypic-and-genotypic-approaches
#19
Maria Bandeira, Vítor Borges, João P Gomes, Aida Duarte, Luisa Jordao
Klebsiella pneumoniae is a prominent etiological agent of healthcare associated infections (HAIs). In this context, multidrug-resistant and biofilm-producing bacteria are of special public health concern due to the difficulties associated with treatment of human infections and eradication from hospital environments. Here, in order to study the impact of medical devices-associated materials on the biofilm dynamics, we performed biofilm phenotypic analyses through a classic and a new scanning electron microscopy (SEM) technique for three multidrug-resistant K...
April 3, 2017: Microorganisms
https://www.readbyqxmd.com/read/28364362/advantages-of-genome-sequencing-by-long-read-sequencer-using-smrt-technology-in-medical-area
#20
REVIEW
Kazuma Nakano, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Shun Ohki, Misuzu Shinzato, Maiko Minami, Tetsuhiro Nakanishi, Kuniko Teruya, Kazuhito Satou, Takashi Hirano
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions...
March 31, 2017: Human Cell
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